Selecting the Texture in Texture Paint Mode
You are needing the Texture Slots tab in the Properties panel in the tool properties. Select the appropriate slot to determine where your paint will go. Here I am using two image textures set to box mapping and one black generated image as a UV mapped stencil between them.

I used an RGB Color Mix node to combine the two textures with Multiply mix mode, so that the rust adds to the original texture instead of replacing it.